Hi Lucia,
yes, this is an issue that I've already seen in a few platforms.
Recently vmtk forks a new process to launch the processing pipe - this allows,
for instance,
to kill a job or to avoid a few issues with PypePad if something goes wrong.
Now, there was probably a glitch in the way things are set up - the tricky bit
is that this
glitch comes out quite erratically and on a few platforms more than others, so
I deferred
its solution.
Now I think I found the culprit of the problem, so I pushed a fix on the
repository.
Since it looks like the error is quite reproducible on your setup, can you
please test it by
updating the code from the repository and let me know?
Thanks!
Luca
On Jun 21, 2012, at 7:22 PM, Lucia Mirabella wrote:
> Hi All,
>
> I'm experiencing a weird problem when using vmtk - development version. I
> started using it last week and I've never had the same problem before (while
> using the binary package 0.9 for mac), but I am not sure where the problem
> comes from.
>
> Basically vmtk scripts work fine generally, but sometimes when I run a
> command, nothing happens - no errors, no usual output. It just seems that the
> command has been disregarded. And if I run the exact same command again
> immediately after, it generally works fine. I paste here below an example,
> where the 2 commands have been run few seconds apart without changing
> anything else in between.
>
> Has any of you had a similar program or an idea on how to solve it? It
> happens also if I run a script containing several chained commands and when
> one fails, the whole script does...
>
> FYI, I'm using vmtk on Mac OS X 10.6.8.
>
> Thanks!
>
> Lucia
>
>
> ibb-yogi-lucia-mac2:time0 lucia$ vmtklevelsetsegmentation -ifile
> image_volume.vti -ofile levelsets_21j.vti
> ibb-yogi-lucia-mac2:time0 lucia$ vmtklevelsetsegmentation -ifile
> image_volume.vti -ofile levelsets_21j.vti
>
> Creating vmtkLevelSetSegmentation instance.
> Automatic piping vmtklevelsetsegmentation
> Parsing options vmtklevelsetsegmentation
> ImageInputFileName = image_volume.vti
> LevelSetsOutputFileName = levelsets_21j.vti
> Explicit piping vmtklevelsetsegmentation
> Input vmtklevelsetsegmentation members:
> Id = 0
> Disabled = 0
> Image = None
> ImageInputFileName = image_volume.vti
> FeatureImage = None
> FeatureImageInputFileName =
> InitializationImage = None
> InitializationImageInputFileName =
> InitialLevelSets = None
> InitialLevelSetsInputFileName =
> LevelSets = None
> LevelSetsInputFileName =
> LevelSetsType = geodesic
> FeatureImageType = gradient
> NegateForInitialization = 0
> SigmoidRemapping = 0
> IsoSurfaceValue = 0.0
> DerivativeSigma = 0.0
> FeatureDerivativeSigma = 0.0
> UpwindFactor = 1.0
> FWHMRadius = [1.0, 1.0, 1.0]
> FWHMBackgroundValue = 0.0
> NumberOfIterations = 0
> PropagationScaling = 0.0
> CurvatureScaling = 0.0
> AdvectionScaling = 1.0
> EdgeWeight = 0.0
> SmoothingIterations = 5
> SmoothingTimeStep = 0.1
> SmoothingConductance = 0.8
> vmtkRenderer = None
> LevelSetsOutputFileName = levelsets_21j.vti
> FeatureImageOutputFileName =
> Reading VTK XML image file.
> Spacing 1.770833 1.770833 2.299997
> Origin 0.000000 0.000000 0.000000
> Dimensions 144 192 32
> Executing vmtklevelsetsegmentation ...
> Please choose initialization type:
> 0: colliding fronts;
> 1: fast marching;
> 2: threshold;
> 3: isosurface;
> 4: seed
> Colliding fronts initialization.
> Please input lower threshold ('n' for none): Please input upper threshold
> ('n' for none): Please place two seeds (click on the image while pressing
> Ctrl).
> Quit renderer
> Displaying.
> Accept initialization? (y/n): Displaying.
> Initialize another branch? (y/n): Please input parameters (type return to
> accept current values, 'e' to end, 'q' to quit):
> Progress: 100%Progress: 100%gationScaling(0.0) CurvatureScaling(0.0)
> AdvectionScaling(1.0)]:
> Displaying.
> Accept result? (y/n): Please input parameters (type return to accept current
> values, 'e' to end, 'q' to quit):
> NumberOfIterations(300) [PropagationScaling(0.0) CurvatureScaling(0.0)
> AdvectionScaling(1.0)]:
> Displaying.
> Accept result? (y/n): Merge branch? (y/n): Displaying.
> Segment another branch? (y/n): Done executing vmtklevelsetsegmentation.
> Writing VTK XML image file.
> Output vmtklevelsetsegmentation members:
> Id = 0
> LevelSets = vtkImageData
> FeatureImage = vtkImageData
>
>
> __________________________________________________
>
> Postdoctoral Fellow, Cardiovascular Fluid Mechanics Laboratory
> Wallace H. Coulter Department of Biomedical Engineering
> Georgia Institute of Technology
> 315 Ferst Drive NW, Parker H. Petit Biotechnology Building
> Atlanta, GA 30332-0363
> E-mail: [email protected]
>
>
>
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